5 protocols
AccessionNameType
P-AGIL-19
hybridization
P-AGIL-18
labeling
P-MTAB-30596
bioassay_data_transformation
Green median signal values from the microarray data were normalized using the quantile method and log2-transformed using the statistical package R (version 2.14.0).



R script for quantile normalization and log2 normalization:

#quant_norm.R



data.only.s <- apply(ldata.only,2,sort)

index.orig <- matrix(1:nrow(ldata.only),nrow=nrow(ldata.only),ncol=ncol(ldata.only))

index.mat <- NULL

for(xi in 1:ncol(ldata.only)) { index.mat <- cbind(index.mat,index.orig[order(ldata.only[,xi]),xi]) }

prot.mean <- apply(data.only.s,1,mean)

data.qnorm <- matrix(prot.mean,nrow=nrow(ldata.only),ncol=ncol(ldata.only))

colnames(data.qnorm) <- colnames(ldata.only)

data.quant <- data.qnorm

for(xi in 1:ncol(ldata.only)){ data.quant[,xi] <- data.quant[,xi][order(index.mat[,xi])] }

data.quant <- log2(data.quant)
P-MTAB-30594
image_acquisition
Microarray slides were scanned using a G2505C microarray scanner (Agilent Technologies) and images were analyzed with Feature Extraction TM software, version 10.5.1.1 (Agilent) according to manufactures protocol (http://www.chem.agilent.com/Library/usermanuals/Public/G4170-90011_miRNA_complete_2.4.pdf)
(Parameters: Scanning hardware = OTHER: G2505C microarray scanner [Agilent], Scanning software = Feature Extraction Software [Agilent])
P-MTAB-30595
nucleic_acid_extraction
Total RNA was isolated from FACS sorted purified leukemic cells with the NucleoSpin miRNA kit (Macherey-Nagel, Düren, Germany) according to manufacturer’s protocol. RNA was concentrated using a vacuum concentrator (SPD111V, Thermo Savant). Final concentration was measured with a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific; Wilmington, DE).
(Parameters: Extracted product = total RNA, Amplification = none)